Merge pull request #12 from domenico-somma/dev

V 0.2.0

.cache/v/cache/lastfailed

@@ -0,0 +1,4 @@
+{
+  "test/test_papillon.py::papillon_Test::test_read_folder": true,
+  "test/test_papillon.py::papillon_Test::test_selected_exist": true
+}

CHANGE.txt

@@ -1,3 +1,14 @@
+v 0.2.0, 24-9-18 -- Major changes:
+Now Pandas 0.23 required
+Now you can keep the genes/isoforms selection in a variable
+Add or compare two subselections
+You can select either gene/isoform significant expressed for at least one condition or not significant at all.
+Plot gene/isoform significant for at least one condition or not significant with continuous and dashed line.
+self.read_db() deprecated
+self.plot() deprecated
+Add check if papillon folder is removed
+Improved code (Single Responsibility Principle)
+
 v 0.1.1, 21-01-18 -- Minor changes: 
 add python 3 restriction, add the function to load directly the cuffdiff files, changed function names: self.read_db() -> self.read_folder() and self.plot() -> self.lineplot(),improved code quality (tried to follow the single responsibility principle), removed some potential bugs. 
 

README.md

@@ -21,7 +21,8 @@ You can use Papillon with any Scientific IDE, and install it using Pypi:
 
 or Anaconda with conda-forge channel:
 
-    conda install -c conda-forge papillon 
+    conda config --add channels conda-forge
+    conda install papillon
 
 ## Usage
 

TO DO.txt

@@ -1,11 +1,10 @@
 * Add Confidence Interval to plot.
-* log10 transformation FPKM values
+* log2 transformation FPKM values
 * Add search isoforms ID option
 * Add barplot
 * plot genes detected/significant as different lines
 * Compare self.selected between two different experiments
 
-* Move plots functions in another py file?
 * Wondering if z_score calc, fusion_gene_id and only_FPKM should be only one function?
 
 * Add Volcano plot
@@ -16,3 +15,6 @@
 * show replicates on lineplot
 * Box plot of FPKM distributions for individual conditions #see cummeRbund
 * Density plot of individual conditions #see cummeRbund
+
+* Add DESEQ2 support
+* Add kallisto/sleuth support